title: High rate of recent transposable element-induced adaptation in Drosophila melanogaster.
abstract: Although transposable elements (TEs) are known to be potent sources of mutation, their contribution to the generation of recent adaptive changes has never been systematically assessed. In this work, we conduct a genome-wide screen for adaptive TE insertions in Drosophila melanogaster that have taken place during or after the spread of this species out of Africa. We determine population frequencies of 902 of the 1,572 TEs in Release 3 of the D. melanogaster genome and identify a set of 13 putatively adaptive TEs. These 13 TEs increased in population frequency sharply after the spread out of Africa. We argue that many of these TEs are in fact adaptive by demonstrating that the regions flanking five of these TEs display signatures of partial selective sweeps. Furthermore, we show that eight out of the 13 putatively adaptive elements show population frequency heterogeneity consistent with these elements playing a role in adaptation to temperate climates. We conclude that TEs have contributed considerably to recent adaptive evolution (one TE-induced adaptation every 200-1,250 y). The majority of these adaptive insertions are likely to be involved in regulatory changes. Our results also suggest that TE-induced adaptations arise more often from standing variants than from new mutations. Such a high rate of TE-induced adaptation is inconsistent with the number of fixed TEs in the D. melanogaster genome, and we discuss possible explanations for this discrepancy.
authors.affiliation: Department of Biology, Stanford University, Stanford, California, United States of America. jgonzalp@stanford.edu
authors.forename: Josefa
authors.initials: J
authors.lastname: González
authors.forename: Kapa
authors.initials: K
authors.lastname: Lenkov
authors.forename: Mikhail
authors.initials: M
authors.lastname: Lipatov
authors.forename: J Michael
authors.initials: JM
authors.lastname: Macpherson
authors.forename: Dmitri A
authors.initials: DA
authors.lastname: Petrov
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D004251:DNA Transposable Elements / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D049750:Genome, Insect; D016254:Mutagenesis, Insertional; D009154:Mutation; D016133:Polymerase Chain Reaction
chemical_list: D004251:DNA Transposable Elements